Package: hapFabia

Version: 1.1.4

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings hapFabia_1.1.4.tar.gz

StartedAt: 2013-01-16 03:27:36 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:29:06 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 90.1 seconds

RetCode: 0

Status:  OK

CheckDir: hapFabia.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.1.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hapFabia’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
iterateIntervals 10.513  0.156  10.674
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘hapFabia’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c interfaceR.c -o interfaceR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
gcc -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 
gcc -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 
gcc -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 
gcc -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 
gcc -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘hapfabia.Rnw’ 
** testing if installed package can be loaded

* DONE (hapFabia)

name	user	system	elapsed
IBDsegment-class	0.716	0.040	0.754
IBDsegmentList-class	0.056	0.004	0.062
IBDsegmentList2excel	0.028	0.000	0.030
analyzeIBDsegments	0.068	0.004	0.073
compareIBDsegmentLists	0.144	0.000	0.143
extractIBDsegments	0.116	0.000	0.116
findDenseRegions	0.028	0.000	0.026
hapFabia	4.768	0.044	4.816
hapFabiaVersion	0.008	0.000	0.009
identifyDuplicates	0.072	0.004	0.079
iterateIntervals	10.513	0.156	10.674
makePipelineFile	0.020	0.000	0.019
matrixPlot	0.016	0.000	0.017
mergeIBDsegmentLists	0.040	0.004	0.043
plotIBDsegment	0.376	0.012	0.389
setAnnotation	0.108	0.004	0.111
setStatistics	0.096	0.000	0.096
sim	0.008	0.000	0.007
simulateIBDsegments	0.008	0.000	0.007
simulateIBDsegmentsFabia	2.760	0.012	2.771
split_sparse_matrix	0.060	0.004	0.063
toolsFactorizationClass	1.736	0.020	1.825
vcftoFABIA	0.332	0.000	0.332